-// Copyright (C) The Lightning Authors. All rights reserved.
-//
-// SPDX-License-Identifier: AGPL-3.0
-
-package lightning
-
-import (
- "bytes"
- "fmt"
- "io"
- "io/ioutil"
- "os"
- "sort"
- "strings"
- "sync"
-
- "gopkg.in/check.v1"
-)
-
-type pipelineSuite struct{}
-
-var _ = check.Suite(&pipelineSuite{})
-
-func (s *pipelineSuite) TestImport(c *check.C) {
- for _, infile := range []string{
- "testdata/pipeline1/",
- "testdata/ref.fasta",
- } {
- c.Logf("TestImport: %s", infile)
- var wg sync.WaitGroup
-
- statsin, importout := io.Pipe()
- wg.Add(1)
- go func() {
- defer wg.Done()
- code := (&importer{}).RunCommand("lightning import", []string{"-local=true", "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags", infile}, bytes.NewReader(nil), importout, os.Stderr)
- c.Check(code, check.Equals, 0)
- importout.Close()
- }()
- statsout := &bytes.Buffer{}
- wg.Add(1)
- go func() {
- defer wg.Done()
- code := (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, statsin, statsout, os.Stderr)
- c.Check(code, check.Equals, 0)
- }()
- wg.Wait()
- c.Logf("%s", statsout.String())
- }
-}
-
-func (s *pipelineSuite) TestImportMerge(c *check.C) {
- libfile := make([]string, 2)
- tmpdir := c.MkDir()
-
- var wg sync.WaitGroup
- for i, infile := range []string{
- "testdata/ref.fasta",
- "testdata/pipeline1/",
- } {
- i, infile := i, infile
- c.Logf("TestImportMerge: %s", infile)
- libfile[i] = fmt.Sprintf("%s/%d.gob", tmpdir, i)
- wg.Add(1)
- go func() {
- defer wg.Done()
- args := []string{"-local=true", "-o=" + libfile[i], "-skip-ooo=true", "-output-tiles", "-tag-library", "testdata/tags"}
- if i == 0 {
- // ref only
- args = append(args, "-save-incomplete-tiles")
- }
- args = append(args, infile)
- code := (&importer{}).RunCommand("lightning import", args, bytes.NewReader(nil), &bytes.Buffer{}, os.Stderr)
- c.Check(code, check.Equals, 0)
- }()
- }
- wg.Wait()
-
- merged := &bytes.Buffer{}
- code := (&merger{}).RunCommand("lightning merge", []string{"-local", libfile[0], libfile[1]}, bytes.NewReader(nil), merged, os.Stderr)
- c.Check(code, check.Equals, 0)
- c.Logf("len(merged) %d", merged.Len())
-
- statsout := &bytes.Buffer{}
- code = (&statscmd{}).RunCommand("lightning stats", []string{"-local"}, bytes.NewReader(merged.Bytes()), statsout, os.Stderr)
- c.Check(code, check.Equals, 0)
- c.Check(statsout.Len() > 0, check.Equals, true)
- c.Logf("%s", statsout.String())
-
- err := os.Mkdir(tmpdir+"/merged", 0777)
- c.Assert(err, check.IsNil)
- c.Check(ioutil.WriteFile(tmpdir+"/merged/library.gob", merged.Bytes(), 0666), check.IsNil)
-
- code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-format", "hgvs", "-input-dir", tmpdir + "/merged", "-output-dir", tmpdir, "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
- c.Check(code, check.Equals, 0)
- hgvsout, err := ioutil.ReadFile(tmpdir + "/out.tsv")
- c.Check(err, check.IsNil)
- c.Check(sortLines(string(hgvsout)), check.Equals, sortLines(`chr1:g.1_3delinsGGC N
-chr1:g.[41T>A];[41=] N
-chr1:g.[42T>A];[42=] N
-chr1:g.[161=];[161A>T] N
-chr1:g.[178=];[178A>T] N
-chr1:g.222_224del N
-chr1:g.[302=];[302_305delinsAAAA] .
-. chr2:g.[1=];[1_3delinsAAA]
-. chr2:g.125_127delinsAAA
-chr2:g.[241_254del];[241=] .
-chr2:g.[258_269delinsAA];[258=] .
-chr2:g.[315C>A];[315=] .
-chr2:g.[470_472del];[470=] .
-chr2:g.[471=];[471G>A] .
-chr2:g.[472=];[472G>A] .
-`))
-
- code = (&exporter{}).RunCommand("lightning export", []string{"-local", "-ref", "testdata/ref.fasta", "-output-dir", tmpdir, "-output-format", "pvcf", "-input-dir", tmpdir + "/merged", "-output-bed", tmpdir + "/export.bed", "-output-per-chromosome=false"}, bytes.NewReader(nil), os.Stderr, os.Stderr)
- c.Check(code, check.Equals, 0)
- vcfout, err := ioutil.ReadFile(tmpdir + "/out.vcf")
- c.Check(err, check.IsNil)
- c.Check(sortLines(string(vcfout)), check.Equals, sortLines(`##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT testdata/pipeline1/input1.1.fasta testdata/pipeline1/input2.1.fasta
-chr1 1 . NNN GGC . . . GT 1/1 0/0
-chr1 41 . T A . . . GT 1/0 0/0
-chr1 42 . T A . . . GT 1/0 0/0
-chr1 161 . A T . . . GT 0/1 0/0
-chr1 178 . A T . . . GT 0/1 0/0
-chr1 221 . TCCA T . . . GT 1/1 0/0
-chr1 302 . TTTT AAAA . . . GT 0/1 0/0
-chr2 1 . TTT AAA . . . GT 0/0 0/1
-chr2 125 . CTT AAA . . . GT 0/0 1/1
-chr2 240 . ATTTTTCTTGCTCTC A . . . GT 1/0 0/0
-chr2 258 . CCTTGTATTTTT AA . . . GT 1/0 0/0
-chr2 315 . C A . . . GT 1/0 0/0
-chr2 469 . GTGG G . . . GT 1/0 0/0
-chr2 471 . G A . . . GT 0/1 0/0
-chr2 472 . G A . . . GT 0/1 0/0
-`))
- bedout, err := ioutil.ReadFile(tmpdir + "/export.bed")
- c.Check(err, check.IsNil)
- c.Logf("%s", string(bedout))
- c.Check(sortLines(string(bedout)), check.Equals, sortLines(`chr1 0 248 0 1000 . 0 224
-chr1 224 372 1 1000 . 248 348
-chr1 348 496 2 1000 . 372 472
-chr1 472 572 3 1000 . 496 572
-chr2 0 248 4 1000 . 0 224
-chr2 224 372 5 750 . 248 348
-chr2 348 496 6 1000 . 372 472
-chr2 472 572 7 1000 . 496 572
-`))
-
- annotateout := &bytes.Buffer{}
- code = (&annotatecmd{}).RunCommand("lightning annotate", []string{"-local", "-variant-hash=true", "-i", tmpdir + "/merged/library.gob"}, bytes.NewReader(nil), annotateout, os.Stderr)
- c.Check(code, check.Equals, 0)
- c.Check(annotateout.Len() > 0, check.Equals, true)
- sorted := sortLines(annotateout.String())
- c.Logf("%s", sorted)
- c.Check(sorted, check.Equals, sortLines(`0,0,8d4fe9a63921b,chr1:g.161A>T
-0,0,8d4fe9a63921b,chr1:g.178A>T
-0,0,8d4fe9a63921b,chr1:g.1_3delinsGGC
-0,0,8d4fe9a63921b,chr1:g.222_224del
-0,0,ba4263ca4199c,chr1:g.1_3delinsGGC
-0,0,ba4263ca4199c,chr1:g.222_224del
-0,0,ba4263ca4199c,chr1:g.41T>A
-0,0,ba4263ca4199c,chr1:g.42T>A
-1,1,139890345dbb8,chr1:g.302_305delinsAAAA
-4,4,cbfca15d241d3,chr2:g.125_127delinsAAA
-4,4,cbfca15d241d3,chr2:g.1_3delinsAAA
-4,4,f5fafe9450b02,chr2:g.241_245delinsAAAAA
-4,4,f5fafe9450b02,chr2:g.291C>A
-4,4,fe9a71a42adb4,chr2:g.125_127delinsAAA
-6,6,e36dce85efbef,chr2:g.471G>A
-6,6,e36dce85efbef,chr2:g.472G>A
-6,6,f81388b184f4a,chr2:g.470_472del
-`))
-}
-
-func sortLines(txt string) string {
- lines := strings.Split(strings.TrimRightFunc(txt, func(c rune) bool { return c == '\n' }), "\n")
- sort.Strings(lines)
- return strings.Join(lines, "\n") + "\n"
-}
projects / lightning.git / blobdiff